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Windows 7: Slow boot after desktop shows but not before, windows x64

So as the title says, for some reason this pc has started to take a few minutes to boot after the desktop shows up but before that the system boots fast.

Have a 1tb seagate sata3 drive as the main drive, yes yes i know i should get a ssd but now is not the time, in the mean time i'd like to figure out what could be causing these slowdowns.
After booting is complete the system runs fine, no direct slowdowns of any sort.

What's been tried:
No viruses, no spyware
Not a bad hdd, been testing that
Removed unnecessary processes/programs from running, most of them set to manual if the system needs them.
Defraged, slight speed increase
Defraged registry, only a few times if it's been needed.

Programs starting at bootup:
Comodo IS
Cacheman, tweaking program
Bluetooth app
Smartdoctor, info app for my graphics card
Asus AI suite II, have uninstalled and reinstalled this app but to no change, tested speed with and without it.

I would suspect your AV software first although Comodo IS is unfamiliar to me so its just a guess having seen similar problems with AVG and Kaspersky IS until bug fixes arrived. If you're feeling brave, disable it and reboot.

Other than that, I've seen issues with plugged in USB devices, so try unplugging everything apart from the mouse and reboot.

So as the title says, for some reason this pc has started to take a few minutes to boot after the desktop shows up but before that the system boots fast.

Have a 1tb seagate sata3 drive as the main drive, yes yes i know i should get a ssd but now is not the time, in the mean time i'd like to figure out what could be causing these slowdowns.
After booting is complete the system runs fine, no direct slowdowns of any sort.

What's been tried:
No viruses, no spyware
Not a bad hdd, been testing that
Removed unnecessary processes/programs from running, most of them set to manual if the system needs them.
Defraged, slight speed increase
Defraged registry, only a few times if it's been needed.

Programs starting at bootup:
Comodo IS
Cacheman, tweaking program
Bluetooth app
Smartdoctor, info app for my graphics card
Asus AI suite II, have uninstalled and reinstalled this app but to no change, tested speed with and without it.

Hopefully i've added enough info to start finding some issues.

1. Uninstall any programs you don't need.
2. Then, go to start and type in msconfig and press enter. Click on the startup tab and disable anything you don't need.
3. Try uninstalling comodo IS and install Microsoft Security Essentials, which can be downloaded here: Microsoft Security Essentials - Microsoft Windows
4. Remove any tweaking programs you have installed on your computer. I don't recommend using tweaking programs.
5. Uninstall any programs you do not need.
6. Go to start and type in disk cleanup then press enter. Once disk cleanup comes up, click on Clean up system files. Check all of the check boxes and then on OK. Note: Cleaning Service Pack backup files will remove the ability to uninstall Service Pack 1.
7. Run disk defragmenter again on all hard drives that you have plugged in.
8 Run a malware scan with Malwarebytes Anti-Malware which can be downloaded here: Download Malwarebytes Anti-Malware 1.70 - FileHippo.com
Note: Malwarebytes will have a ckeckbox check at the end of the installation that says " Enable free Trial of Malwarebytes Pro." Be sure to uncheck that checkbox.
Also, if you disabled any Windows services or set them to manual, set them back to what they originally were.

So as the title says, for some reason this pc has started to take a few minutes to boot after the desktop shows up but before that the system boots fast.

Have a 1tb seagate sata3 drive as the main drive, yes yes i know i should get a ssd but now is not the time, in the mean time i'd like to figure out what could be causing these slowdowns.
After booting is complete the system runs fine, no direct slowdowns of any sort.

What's been tried:
No viruses, no spyware
Not a bad hdd, been testing that
Removed unnecessary processes/programs from running, most of them set to manual if the system needs them.
Defraged, slight speed increase
Defraged registry, only a few times if it's been needed.

Programs starting at bootup:
Comodo IS
Cacheman, tweaking program
Bluetooth app
Smartdoctor, info app for my graphics card
Asus AI suite II, have uninstalled and reinstalled this app but to no change, tested speed with and without it.

Hopefully i've added enough info to start finding some issues.

1. Uninstall any programs you don't need.
2. Then, go to start and type in msconfig and press enter. Click on the startup tab and disable anything you don't need.
3. Try uninstalling comodo IS and install Microsoft Security Essentials, which can be downloaded here: Microsoft Security Essentials - Microsoft Windows
4. Remove any tweaking programs you have installed on your computer. I don't recommend using tweaking programs.
5. Uninstall any programs you do not need.
6. Go to start and type in disk cleanup then press enter. Once disk cleanup comes up, click on Clean up system files. Check all of the check boxes and then on OK. Note: Cleaning Service Pack backup files will remove the ability to uninstall Service Pack 1.
7. Run disk defragmenter again on all hard drives that you have plugged in.
8 Run a malware scan with Malwarebytes Anti-Malware which can be downloaded here: Download Malwarebytes Anti-Malware 1.70 - FileHippo.com
Note: Malwarebytes will have a ckeckbox check at the end of the installation that says " Enable free Trial of Malwarebytes Pro." Be sure to uncheck that checkbox.
Also, if you disabled any Windows services or set them to manual, set them back to what they originally were.

1. already been done.

2. same

3. as far as i know it's not comodo that's the issue, it's very light on the resources and not everything is even enabled on it and i don't plan on going to another av suite.

4. i've used cacheman for years, thinking back to windows 98, it's safe and does improve the speed of the systems rather nicely.

Hum never had a problem myself with either CIS or KIS but all things being equal....

Bitdefender is pretty light on if you are looking for a free AV.

Another option is go through this tutorial if you don't mind losing a bit of the "bling" like transparency.

Optimize Windows 7 < Point 7 method 3 is very useful - I leave the OS and security ticked as a precaution in Startup. But the other points are as good for loosening up the machine:)

Not planing on another antivirus app and from what i know i've already loosend up this machine as much as i can so something is slowing it down at boot BUT it runs fine for most of the time after, on ocation i can hear the hd go up to full use when say looking at a website "seldom happens" or starting another app but usualy it's just safe sailing heh.

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